Index _ | A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W _ __ax_set_invisible() (birl.utilities.drawing.RadarChart class method) __check_exist_path() (birl.utilities.experiments.Experiment method) __check_exist_regist() (birl.benchmark.ImRegBenchmark method) __create_folder() (birl.utilities.experiments.Experiment method) __draw_curve() (birl.utilities.drawing.RadarChart method) __draw_labels() (birl.utilities.drawing.RadarChart method) __execute_method() (birl.benchmark.ImRegBenchmark method) __export_df_experiments() (birl.benchmark.ImRegBenchmark method) __images_preprocessing() (birl.benchmark.ImRegBenchmark method) __realign_polar_xtick() (birl.utilities.drawing.RadarChart class method) __remove_pproc_images() (birl.benchmark.ImRegBenchmark method) _absolute_path() (birl.benchmark.ImRegBenchmark method) _check_required_params() (birl.utilities.experiments.Experiment method) _clean_images() (in module bm_experiments.bm_comp_perform) _clear_after_registration() (birl.benchmark.ImRegBenchmark class method) (birl.bm_template.BmTemplate method) (bm_experiments.bm_ANTs.BmANTs method) (bm_experiments.bm_DROP.BmDROP method) (bm_experiments.bm_DROP2.BmDROP2 method) (bm_experiments.bm_elastix.BmElastix method) (bm_experiments.bm_RVSS.BmRVSS method) _copy_config_to_expt() (birl.benchmark.ImRegBenchmark method) _df_drop_unnamed() (in module birl.benchmark) _evaluate() (birl.benchmark.ImRegBenchmark method) (birl.utilities.experiments.Experiment class method) _execute_img_registration() (birl.benchmark.ImRegBenchmark method) _extract_execution_time() (birl.benchmark.ImRegBenchmark method) (birl.bm_template.BmTemplate method) (bm_experiments.bm_ANTsPy.BmANTsPy method) (bm_experiments.bm_rNiftyReg.BmRNiftyReg method) _extract_warped_image_landmarks() (birl.benchmark.ImRegBenchmark class method) (birl.bm_template.BmTemplate method) (bm_experiments.bm_ANTs.BmANTs method) (bm_experiments.bm_ANTsPy.BmANTsPy method) (bm_experiments.bm_bUnwarpJ.BmUnwarpJ method) (bm_experiments.bm_DROP.BmDROP method) (bm_experiments.bm_DROP2.BmDROP2 method) (bm_experiments.bm_elastix.BmElastix method) (bm_experiments.bm_rNiftyReg.BmRNiftyReg method) (bm_experiments.bm_RVSS.BmRVSS method) _gene_out_path() (in module birl.utilities.data_io) _generate_regist_command() (birl.benchmark.ImRegBenchmark method) (birl.bm_template.BmTemplate method) (bm_experiments.bm_ANTs.BmANTs method) (bm_experiments.bm_ANTsPy.BmANTsPy method) (bm_experiments.bm_bUnwarpJ.BmUnwarpJ method) (bm_experiments.bm_DROP.BmDROP method) (bm_experiments.bm_DROP2.BmDROP2 method) (bm_experiments.bm_elastix.BmElastix method) (bm_experiments.bm_rNiftyReg.BmRNiftyReg method) (bm_experiments.bm_RVSS.BmRVSS method) _get_path_reg_dir() (birl.benchmark.ImRegBenchmark method) _get_paths() (birl.benchmark.ImRegBenchmark method) _get_ram() (in module birl.utilities.experiments) _image_diag() (birl.benchmark.ImRegBenchmark class method) _list_colors() (in module birl.utilities.drawing) _load_data() (birl.benchmark.ImRegBenchmark method) (birl.utilities.experiments.Experiment class method) _load_landmarks() (birl.benchmark.ImRegBenchmark class method) _load_warped_image() (birl.benchmark.ImRegBenchmark class method) _parse_regist_results() (birl.benchmark.ImRegBenchmark method) _perform_registration() (birl.benchmark.ImRegBenchmark method) _prepare() (birl.bm_template.BmTemplate method) (birl.utilities.experiments.Experiment class method) (bm_experiments.bm_ANTs.BmANTs method) (bm_experiments.bm_ANTsPy.BmANTsPy method) (bm_experiments.bm_bUnwarpJ.BmUnwarpJ method) (bm_experiments.bm_DROP.BmDROP method) (bm_experiments.bm_elastix.BmElastix method) (bm_experiments.bm_rNiftyReg.BmRNiftyReg method) (bm_experiments.bm_RVSS.BmRVSS method) _prepare_images() (in module bm_experiments.bm_comp_perform) _prepare_img_registration() (birl.benchmark.ImRegBenchmark class method) (birl.bm_template.BmTemplate method) (bm_experiments.bm_ANTs.BmANTs method) (bm_experiments.bm_DROP.BmDROP method) (bm_experiments.bm_DROP2.BmDROP2 method) _rand_float() (in module bm_experiments.bm_comp_perform) _relativize_path() (birl.benchmark.ImRegBenchmark method) _run() (birl.benchmark.ImRegBenchmark method) (birl.utilities.experiments.Experiment class method) _summarise() (birl.benchmark.ImRegBenchmark method) (birl.utilities.experiments.Experiment class method) _visual_image_move_warp_lnds_move_warp() (birl.benchmark.ImRegBenchmark class method) _visual_image_move_warp_lnds_ref_warp() (birl.benchmark.ImRegBenchmark class method) A aggregate_user_score_timeline() (in module birl.utilities.evaluate) arg_parse_params() (in module bm_dataset.convert_tiff2png) (in module bm_dataset.create_real_synth_dataset) (in module bm_dataset.crop_tissue_images) (in module bm_dataset.generate_regist_pairs) (in module bm_dataset.rescale_tissue_images) (in module bm_dataset.rescale_tissue_landmarks) (in module bm_dataset.split_images_two_tissues) (in module bm_experiments.bm_comp_perform) args_expand_images() (in module birl.utilities.dataset) args_expand_parse_images() (in module birl.utilities.dataset) B birl module birl.benchmark module birl.bm_template module birl.utilities module birl.utilities.data_io module birl.utilities.dataset module birl.utilities.drawing module birl.utilities.evaluate module birl.utilities.experiments module birl.utilities.registration module bm_dataset module bm_dataset.convert_tiff2png module bm_dataset.create_real_synth_dataset module bm_dataset.crop_tissue_images module bm_dataset.generate_regist_pairs module bm_dataset.rescale_tissue_images module bm_dataset.rescale_tissue_landmarks module bm_dataset.split_images_two_tissues module bm_experiments module bm_experiments.bm_ANTs module bm_experiments.bm_ANTsPy module bm_experiments.bm_bUnwarpJ module bm_experiments.bm_comp_perform module bm_experiments.bm_DROP module bm_experiments.bm_DROP2 module bm_experiments.bm_elastix module bm_experiments.bm_rNiftyReg module bm_experiments.bm_RVSS module bm_experiments.evaluate_experiment module BmANTs (class in bm_experiments.bm_ANTs) BmANTsPy (class in bm_experiments.bm_ANTsPy) BmDROP (class in bm_experiments.bm_DROP) BmDROP2 (class in bm_experiments.bm_DROP2) BmElastix (class in bm_experiments.bm_elastix) BmRNiftyReg (class in bm_experiments.bm_rNiftyReg) BmRVSS (class in bm_experiments.bm_RVSS) BmTemplate (class in birl.bm_template) BmUnwarpJ (class in bm_experiments.bm_bUnwarpJ) C COL_IMAGE_DIAGONAL (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_EXT_TEMP (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_MOVE (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_MOVE_NII (bm_experiments.bm_ANTs.BmANTs attribute) COL_IMAGE_MOVE_WARP (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_REF (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_REF_NII (bm_experiments.bm_ANTs.BmANTs attribute) COL_IMAGE_REF_WARP (birl.benchmark.ImRegBenchmark attribute) COL_IMAGE_SIZE (birl.benchmark.ImRegBenchmark attribute) COL_NB_LANDMARKS_INPUT (birl.benchmark.ImRegBenchmark attribute) COL_NB_LANDMARKS_WARP (birl.benchmark.ImRegBenchmark attribute) COL_PAIRED_LANDMARKS (in module birl.benchmark) COL_POINTS_MOVE (birl.benchmark.ImRegBenchmark attribute) COL_POINTS_MOVE_WARP (birl.benchmark.ImRegBenchmark attribute) COL_POINTS_REF (birl.benchmark.ImRegBenchmark attribute) COL_POINTS_REF_WARP (birl.benchmark.ImRegBenchmark attribute) COL_REG_DIR (birl.benchmark.ImRegBenchmark attribute) COL_ROBUSTNESS (birl.benchmark.ImRegBenchmark attribute) COL_STATUS (birl.benchmark.ImRegBenchmark attribute) COL_TIME (birl.benchmark.ImRegBenchmark attribute) COL_TIME_CONVERT (bm_experiments.bm_DROP.BmDROP attribute) COL_TIME_PREPROC (birl.benchmark.ImRegBenchmark attribute) COMMAND_REGISTER (bm_experiments.bm_ANTs.BmANTs attribute) (bm_experiments.bm_DROP2.BmDROP2 attribute) COMMAND_REGISTRATION (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) (bm_experiments.bm_elastix.BmElastix attribute) (bm_experiments.bm_RVSS.BmRVSS attribute) COMMAND_TRANSFORMATION (bm_experiments.bm_elastix.BmElastix attribute) COMMAND_WARP_IMAGE (bm_experiments.bm_ANTs.BmANTs attribute) COMMAND_WARP_LANDMARKS (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) (bm_experiments.bm_RVSS.BmRVSS attribute) COMMAND_WARP_POINTS (bm_experiments.bm_ANTs.BmANTs attribute) common_landmarks() (in module birl.utilities.dataset) compute_affine_transf_diff() (in module birl.utilities.evaluate) compute_bounding_polygon() (in module birl.utilities.dataset) compute_convex_hull() (in module birl.utilities.dataset) compute_half_polygon() (in module birl.utilities.dataset) compute_matrix_user_ranking() (in module birl.utilities.evaluate) compute_ranking() (in module birl.utilities.evaluate) compute_registration_accuracy() (birl.benchmark.ImRegBenchmark class method) compute_registration_statistic() (birl.benchmark.ImRegBenchmark class method) compute_target_regist_error_statistic() (in module birl.utilities.evaluate) compute_tre() (in module birl.utilities.evaluate) compute_tre_robustness() (in module birl.utilities.evaluate) computer_info() (in module birl.utilities.experiments) convert_image() (in module bm_dataset.convert_tiff2png) convert_image_from_mhd() (in module birl.utilities.data_io) convert_image_from_nifti() (in module birl.utilities.data_io) convert_image_to_mhd() (in module birl.utilities.data_io) convert_image_to_nifti() (in module birl.utilities.data_io) convert_image_to_nifti_gray() (in module birl.utilities.data_io) convert_landmarks_from_itk() (in module birl.utilities.dataset) convert_landmarks_to_itk() (in module birl.utilities.dataset) convert_ndarray2image() (in module birl.utilities.data_io) CONVERT_RGB (in module birl.utilities.dataset) COVER_COLUMNS (birl.benchmark.ImRegBenchmark attribute) COVER_COLUMNS_EXT (birl.benchmark.ImRegBenchmark attribute) COVER_COLUMNS_WRAP (birl.benchmark.ImRegBenchmark attribute) CPU_COUNT (in module birl.utilities.experiments) create_basic_parser() (in module birl.utilities.experiments) create_experiment_folder() (in module birl.utilities.experiments) create_figure() (in module birl.utilities.drawing) create_folder() (in module birl.utilities.data_io) create_parser() (in module bm_experiments.evaluate_experiment) crop_image() (in module bm_dataset.crop_tissue_images) CUT_DIMENSION (in module bm_dataset.split_images_two_tissues) D dataset_expand_landmarks() (in module bm_dataset.rescale_tissue_landmarks) dataset_scale_landmarks() (in module bm_dataset.rescale_tissue_landmarks) DEFAULT_PARAMS (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) (bm_experiments.bm_RVSS.BmRVSS attribute) deform_image_landmarks() (in module bm_dataset.create_real_synth_dataset) detect_binary_blocks() (in module birl.utilities.dataset) dict_deep_update() (in module birl.utilities.experiments) DIR_INPUTS (bm_experiments.bm_RVSS.BmRVSS attribute) DIR_OUTPUTS (bm_experiments.bm_RVSS.BmRVSS attribute) draw_heatmap() (in module birl.utilities.drawing) draw_image_landmarks() (in module bm_dataset.create_real_synth_dataset) draw_image_points() (in module birl.utilities.drawing) draw_images_warped_landmarks() (in module birl.utilities.drawing) draw_landmarks_origin_target_warped() (in module birl.utilities.drawing) draw_matrix_user_ranking() (in module birl.utilities.drawing) draw_scatter_double_scale() (in module birl.utilities.drawing) E effective_decimals() (in module birl.utilities.drawing) estimate_affine_transform() (in module birl.utilities.registration) estimate_scaling() (in module birl.utilities.dataset) exec_commands() (in module birl.utilities.experiments) EXEC_ELASTIX (bm_experiments.bm_elastix.BmElastix attribute) EXEC_REGISTRATION (bm_experiments.bm_ANTs.BmANTs attribute) EXEC_TRANSFORM_IMAGE (bm_experiments.bm_ANTs.BmANTs attribute) EXEC_TRANSFORM_POINTS (bm_experiments.bm_ANTs.BmANTs attribute) EXEC_TRANSFX (bm_experiments.bm_elastix.BmElastix attribute) EXECUTE_TIMEOUT (birl.benchmark.ImRegBenchmark attribute) (bm_experiments.bm_ANTs.BmANTs attribute) expand_random_warped_landmarks() (in module bm_dataset.rescale_tissue_landmarks) Experiment (class in birl.utilities.experiments) export_figure() (in module birl.utilities.drawing) export_image_landmarks() (in module bm_dataset.create_real_synth_dataset) export_summary_results() (in module birl.benchmark) extend_landmarks() (in module bm_dataset.rescale_tissue_landmarks) extend_parse() (birl.benchmark.ImRegBenchmark static method) (birl.bm_template.BmTemplate static method) (bm_experiments.bm_ANTs.BmANTs static method) (bm_experiments.bm_ANTsPy.BmANTsPy static method) (bm_experiments.bm_bUnwarpJ.BmUnwarpJ static method) (bm_experiments.bm_DROP.BmDROP static method) (bm_experiments.bm_elastix.BmElastix static method) (bm_experiments.bm_rNiftyReg.BmRNiftyReg static method) (bm_experiments.bm_RVSS.BmRVSS static method) extract_landmarks_shift_from_mhd() (bm_experiments.bm_DROP.BmDROP static method) extract_landmarks_shift_from_nifty() (bm_experiments.bm_DROP2.BmDROP2 static method) F FILE_LOGS (in module birl.utilities.experiments) filter_paired_landmarks() (in module birl.benchmark) find_largest_object() (in module birl.utilities.dataset) find_split_objects() (in module birl.utilities.dataset) FORMAT_DATE_TIME (in module birl.utilities.experiments) G generate_deformation_field_gauss() (in module bm_dataset.create_real_synth_dataset) generate_deformation_field_rbf() (in module bm_dataset.create_real_synth_dataset) generate_pairing() (in module birl.utilities.dataset) generate_pairs() (in module bm_dataset.generate_regist_pairs) generate_random_points_inside() (in module bm_dataset.rescale_tissue_landmarks) get_affine_components() (in module birl.utilities.registration) get_close_diag_corners() (in module birl.utilities.dataset) get_name() (in module bm_dataset.create_real_synth_dataset) get_nb_workers() (in module birl.utilities.experiments) grouping_cumulative() (in module birl.utilities.evaluate) H histogram_match_cumulative_cdf() (in module birl.utilities.dataset) I image_color_shift_hue() (in module bm_dataset.create_real_synth_dataset) IMAGE_EXTENSIONS (in module birl.utilities.dataset) image_histogram_matching() (in module birl.utilities.dataset) image_resize() (in module birl.utilities.data_io) image_sizes() (in module birl.utilities.data_io) ImRegBenchmark (class in birl.benchmark) inside_polygon() (in module birl.utilities.dataset) io_image_decorate() (in module birl.utilities.data_io) is_iterable() (in module birl.utilities.experiments) is_point_above_line() (in module birl.utilities.dataset) is_point_in_quadrant_left() (in module birl.utilities.dataset) is_point_inside_perpendicular() (in module birl.utilities.dataset) ITERABLE_TYPES (in module birl.utilities.experiments) iterate_mproc_map() (in module birl.utilities.experiments) L LANDMARK_COORDS (in module birl.utilities.data_io) line_angle_2d() (in module birl.utilities.dataset) list_sub_folders() (in module birl.utilities.dataset) load_config_args() (in module birl.utilities.data_io) load_config_yaml() (in module birl.utilities.data_io) load_image() (in module birl.utilities.data_io) load_landmarks() (in module birl.utilities.data_io) load_landmarks_csv() (in module birl.utilities.data_io) load_landmarks_pts() (in module birl.utilities.data_io) load_large_image() (in module birl.utilities.dataset) load_largest_scale() (in module bm_dataset.rescale_tissue_landmarks) LOG_FILE_FORMAT (in module birl.utilities.experiments) M main() (birl.benchmark.ImRegBenchmark class method) (in module bm_dataset.convert_tiff2png) (in module bm_dataset.create_real_synth_dataset) (in module bm_dataset.crop_tissue_images) (in module bm_dataset.generate_regist_pairs) (in module bm_dataset.rescale_tissue_images) (in module bm_dataset.rescale_tissue_landmarks) (in module bm_dataset.split_images_two_tissues) (in module bm_experiments.bm_comp_perform) (in module bm_experiments.evaluate_experiment) MAX_FIGURE_SIZE (in module birl.utilities.drawing) MAX_IMAGE_DIAGONAL (bm_experiments.bm_DROP.BmDROP attribute) MAX_IMAGE_SIZE (in module birl.utilities.dataset) measure_registration_parallel() (in module bm_experiments.bm_comp_perform) measure_registration_single() (in module bm_experiments.bm_comp_perform) module birl birl.benchmark birl.bm_template birl.utilities birl.utilities.data_io birl.utilities.dataset birl.utilities.drawing birl.utilities.evaluate birl.utilities.experiments birl.utilities.registration bm_dataset bm_dataset.convert_tiff2png bm_dataset.create_real_synth_dataset bm_dataset.crop_tissue_images bm_dataset.generate_regist_pairs bm_dataset.rescale_tissue_images bm_dataset.rescale_tissue_landmarks bm_dataset.split_images_two_tissues bm_experiments bm_experiments.bm_ANTs bm_experiments.bm_ANTsPy bm_experiments.bm_bUnwarpJ bm_experiments.bm_comp_perform bm_experiments.bm_DROP bm_experiments.bm_DROP2 bm_experiments.bm_elastix bm_experiments.bm_rNiftyReg bm_experiments.bm_RVSS bm_experiments.evaluate_experiment N NAME_CONFIG_YAML (birl.utilities.experiments.Experiment attribute) NAME_CSV_REGISTRATION_PAIRS (birl.benchmark.ImRegBenchmark attribute) NAME_CSV_RESULTS (in module bm_experiments.evaluate_experiment) NAME_CSV_SUMMARY (in module bm_experiments.evaluate_experiment) NAME_FILE_IMAGE (bm_experiments.bm_rNiftyReg.BmRNiftyReg attribute) NAME_FILE_LANDMARKS (bm_experiments.bm_rNiftyReg.BmRNiftyReg attribute) NAME_FILE_TIME (bm_experiments.bm_rNiftyReg.BmRNiftyReg attribute) NAME_IMAGE_MOVE_WARP_POINTS (birl.benchmark.ImRegBenchmark attribute) NAME_IMAGE_REF_POINTS_WARP (birl.benchmark.ImRegBenchmark attribute) NAME_IMAGE_REF_WARP (birl.benchmark.ImRegBenchmark attribute) NAME_IMAGE_WARPED (bm_experiments.bm_ANTsPy.BmANTsPy attribute) (bm_experiments.bm_elastix.BmElastix attribute) NAME_IMAGE_WARPED_VISUAL (birl.benchmark.ImRegBenchmark attribute) NAME_LANDMARKS (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) NAME_LANDMARKS_WARPED (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) NAME_LNDS_WARPED (bm_experiments.bm_ANTsPy.BmANTsPy attribute) (bm_experiments.bm_elastix.BmElastix attribute) NAME_LOG_REGISTRATION (birl.benchmark.ImRegBenchmark attribute) NAME_RESULTS_CSV (birl.benchmark.ImRegBenchmark attribute) (birl.utilities.experiments.Experiment attribute) NAME_RESULTS_TXT (birl.benchmark.ImRegBenchmark attribute) (birl.utilities.experiments.Experiment attribute) NAME_TIME_EXEC (bm_experiments.bm_ANTsPy.BmANTsPy attribute) NAME_TRANSF_DIRECT (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) NAME_TRANSF_INVERSE (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) NAME_TXT_SUMMARY (in module bm_experiments.evaluate_experiment) NB_WORKERS (in module bm_experiments.evaluate_experiment) NB_WORKERS_USED (birl.benchmark.ImRegBenchmark attribute) norm_angle() (in module birl.utilities.dataset) (in module birl.utilities.registration) O overlap_two_images() (in module birl.utilities.drawing) P parse_arg_params() (in module birl.utilities.experiments) parse_path_scale() (in module birl.utilities.dataset) parse_warped_points() (bm_experiments.bm_elastix.BmElastix static method) PATH_IJ_SCRIPTS (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) PATH_SCRIPT_REGISTRATION (bm_experiments.bm_RVSS.BmRVSS attribute) PATH_SCRIPT_REGISTRATION_BASE (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) PATH_SCRIPT_REGISTRATION_SIFT (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) PATH_SCRIPT_WARP_LANDMARKS (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) (bm_experiments.bm_RVSS.BmRVSS attribute) perform_deform_export() (in module bm_dataset.create_real_synth_dataset) project_object_edge() (in module birl.utilities.dataset) R RadarChart (class in birl.utilities.drawing) REEXP_FOLDER_SCALE (in module birl.utilities.dataset) register_image_pair() (in module bm_experiments.bm_comp_perform) release_logger_files() (in module birl.utilities.experiments) REQUIRED_PARAMS (birl.benchmark.ImRegBenchmark attribute) (birl.bm_template.BmTemplate attribute) (birl.utilities.experiments.Experiment attribute) (bm_experiments.bm_ANTs.BmANTs attribute) (bm_experiments.bm_ANTsPy.BmANTsPy attribute) (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) (bm_experiments.bm_DROP.BmDROP attribute) (bm_experiments.bm_elastix.BmElastix attribute) (bm_experiments.bm_rNiftyReg.BmRNiftyReg attribute) (bm_experiments.bm_RVSS.BmRVSS attribute) REQUIRED_PARAMS_BUNWARPJ (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) REQUIRED_PARAMS_RVSS (bm_experiments.bm_RVSS.BmRVSS attribute) REQUIRED_PARAMS_SIFT (bm_experiments.bm_bUnwarpJ.BmUnwarpJ attribute) run() (birl.utilities.experiments.Experiment method) S save_config_yaml() (in module birl.utilities.data_io) save_image() (in module birl.utilities.data_io) save_landmarks() (in module birl.utilities.data_io) save_landmarks_csv() (in module birl.utilities.data_io) save_landmarks_pts() (in module birl.utilities.data_io) save_large_image() (in module birl.utilities.dataset) scale_image() (in module bm_dataset.rescale_tissue_images) scale_large_images_landmarks() (in module birl.utilities.dataset) scale_set_landmarks() (in module bm_dataset.rescale_tissue_landmarks) SCALE_SIZE (in module bm_dataset.split_images_two_tissues) set_experiment_logger() (in module birl.utilities.experiments) simplify_polygon() (in module birl.utilities.dataset) split_image() (in module bm_dataset.split_images_two_tissues) STR_LOG_FORMAT (in module birl.utilities.experiments) string_dict() (in module birl.utilities.experiments) T TISSUE_CONTENT (in module birl.utilities.dataset) transform_points() (in module birl.utilities.registration) try_decorator() (in module birl.utilities.experiments) U update_path() (in module birl.utilities.data_io) update_paths() (in module birl.utilities.experiments) V visualise_registration() (birl.benchmark.ImRegBenchmark class method) W wrap_scale_image() (in module bm_dataset.rescale_tissue_images)